Let me straight and clear the misunderstanding here,
First, it was Soekarno who want's to easy the burden of Pakistan Navy when they are in war against India by threatening to attack Andaman and Nicobar islands. The invasion forces will be diverted from the SATGAS Mandala task force who initially being prepared to retake Papua islands from the Dutch forces. But when the Confrontation against England, Malaysia, Australia and New Zealand is looming and reaching the boiling points and economic constraint hampered Indonesian military expenditure and resources, the prospect for Indonesia to capturing Andaman and Nicobar is nearing zero in which Indonesia had no fund and resources to bet against India just for some sentimental idea.
Soeharto on other hands is quite pragmatic and doesn't share the expansionist value of Soekarno, he instead choosing to rebuilt Indonesian economy and left the rogue states way of Soekarno and building institutional-ism and regionalism among ASEAN countries but he is still wary about India and Soviet close cooperation so he is not too fond about India either.
And there is no one sane person in modern Indonesia right now had questioning about the legitimacy of India over Nicobar and Andaman